8TSM | pdb_00008tsm

Crystal structure of chicken Netrin-1 LN LE1-2

PDB DOI: https://doi.org/10.2210/pdb8TSM/pdb

Classification: SIGNALING PROTEIN
Organism(s): Gallus gallus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-11 Released: 2024-08-28
Deposition Author(s): Heide, F., Rafiei, F., Stetefeld, J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free:
0.319 (Depositor), 0.320 (DCC)
R-Value Work:
0.312 (Depositor), 0.320 (DCC)
R-Value Observed:
0.312 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Investigation of the dynamic nature of Netrin-1 on dependence receptor signaling

Rafiei, F., Heide, F., Legare, S., Gabir, H., Padilla-Meier, P., Meier, M., Koch, M., Stetefeld, J.

To be published.

Macromolecule Content

Total Structure Weight: 44.68 kDa
Atom Count: 2,846
Modeled Residue Count: 354
Deposited Residue Count: 393
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A	393	Gallus gallus	Mutation(s): 0 Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus) Explore Q90922 Go to UniProtKB: Q90922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q90922
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.319 (Depositor), 0.320 (DCC)
R-Value Work: 0.312 (Depositor), 0.320 (DCC)
R-Value Observed: 0.312 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.413	α = 90
b = 112.413	β = 90
c = 242.644	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.